def __init__(self, file_, *args, **kw):
super(LoadClassifierDialog, self).__init__(*args, **kw)
uifile = splitext(__file__)[0] + ".ui"
loadUI(uifile, self)
self.setResult(-1)
self._file = file_
self.descriptions = dict()
self.progressBar.hide()
self.loadFileInfo(file_)
self.classifier_name.currentIndexChanged[str].connect(self.onClassifierChanged)
def __init__(self, *args, **kw):
super(SeededMaskWidget, self).__init__(*args, **kw)
loadUI(splitext(__file__)[0]+'.ui', self)
self.norm.setText("Intesity Norm. ")
self.mtype.addItems(SeededMask.masks())
self.mtype.currentTextChanged.connect(
self.onMtypeChanged)
self.onMtypeChanged(self.mtype.currentText())
self.inner.valueChanged.connect(self.onInnerValueChanged)
self.outer.valueChanged.connect(self.onOuterValueChanged)
def __init__(self, file_, *args, **kw):
super(LoadClassifierDialog, self).__init__(*args, **kw)
uifile = splitext(__file__)[0] + ".ui"
loadUI(uifile, self)
self.setResult(-1)
self._file = file_
self.descriptions = dict()
self.progressBar.hide()
self.loadFileInfo(file_)
self.classifier_name.currentIndexChanged[str].connect(
self.onClassifierChanged)
def __init__(self, classifier, labels, sample_info, description,
*args, **kw):
super(SaveClassifierDialog, self).__init__(*args, **kw)
uifile = splitext(__file__)[0] + ".ui"
loadUI(uifile, self)
self._path = None
self._description.setPlainText(description)
self.classifier = classifier
self.labels = labels
self.sinfo = sample_info
self.name = classifier.name.replace(" ", "_").lower()
self._name.selectAll()
def __init__(self, *args, **kw):
super(AtPreferencesDialog, self).__init__(*args, **kw)
loadUI(splitext(__file__)[0] + '.ui', self)
self.setWindowTitle("Preferences")
self._compopts_old = dict()
self.loadSettings()
self.accepted.connect(self.saveSettings)
self.hdf_compression.currentIndexChanged[str].connect(
self.updateCompressionOptions)
self.hdf_compopts.currentIndexChanged[str].connect(
self.compoptsUpdated)
def __init__(self, *args, **kw):
super(AtPreferencesDialog, self).__init__(*args, **kw)
loadUI(splitext(__file__)[0]+'.ui', self)
self.setWindowTitle("Preferences")
self._compopts_old = dict()
self.loadSettings()
self.accepted.connect(self.saveSettings)
self.hdf_compression.currentIndexChanged[str].connect(
self.updateCompressionOptions)
self.hdf_compopts.currentIndexChanged[str].connect(
self.compoptsUpdated)
def __init__(self, *args, **kw):
super(ImportDialog, self).__init__(*args, **kw)
loadUI(splitext(__file__)[0] + '.ui', self)
for name, scn in FileScanner.iterclasses():
self.structType.addItem(scn.icon(), name)
self.structType.setIconSize(QtCore.QSize(48, 24))
self.metadata = None
self._files = None
self.progressBar.hide()
self.segdlg = SegmentationDialog(self)
self.segdlg.hide()
self.thread = AtThread(self)
self.viewer.setSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding,
QtWidgets.QSizePolicy.MinimumExpanding)
self.cbar = ChannelBar(self, self.viewer)
self.cbox.addWidget(self.cbar)
self.cbar.newPixmap.connect(self.viewer.showPixmap,
Qt.DirectConnection)
self.cbar.newContourImage.connect(self.viewer.contourImage)
self.dataFileBtn.clicked.connect(self.onOpenOutFile)
self.imageDirBtn.clicked.connect(self.onOpenImageDir)
self.startBtn.clicked.connect(self.raw2hdf)
self.closeBtn.clicked.connect(self.close)
self.closeBtn.clicked.connect(self.cbar.clear)
self.segmentationBtn.clicked.connect(self.onSegmentationBtn)
self.slider.newValue.connect(self.showObjects)
self.slider.valueChanged.connect(self.showImage)
self.slider.sliderReleased.connect(self.showObjects)
self.slider.sliderPressed.connect(self.cbar.clearContours)
self.contoursCb.stateChanged.connect(self.onContours)
self.showBBoxes.stateChanged.connect(self.onBBoxes)
self.showBBoxes.stateChanged.connect(self.showObjects)
self.segdlg.paramsChanged.connect(self.showObjects)
self.segdlg.refreshBtn.clicked.connect(self.showObjects)
self.segdlg.imageUpdate.connect(self.showImage)
self.segdlg.activateChannels.connect(self.cbar.activateChannels)
self.segdlg.changeColor.connect(self.cbar.setColor)
self.nextBtn.clicked.connect(self.onNextBtn)
self.prevBtn.clicked.connect(self.onPrevBtn)
def __init__(self, *args, **kw):
super(ImportDialog, self).__init__(*args, **kw)
loadUI(splitext(__file__)[0]+'.ui', self)
for name, scn in FileScanner.iterclasses():
self.structType.addItem(scn.icon(), name)
self.structType.setIconSize(QtCore.QSize(48, 24))
self.metadata = None
self._files = None
self.progressBar.hide()
self.segdlg = SegmentationDialog(self)
self.segdlg.hide()
self.thread = AtThread(self)
self.viewer.setSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding,
QtWidgets.QSizePolicy.MinimumExpanding)
self.cbar = ChannelBar(self, self.viewer)
self.cbox.addWidget(self.cbar)
self.cbar.newPixmap.connect(self.viewer.showPixmap,
Qt.DirectConnection)
self.cbar.newContourImage.connect(self.viewer.contourImage)
self.dataFileBtn.clicked.connect(self.onOpenOutFile)
self.imageDirBtn.clicked.connect(self.onOpenImageDir)
self.startBtn.clicked.connect(self.raw2hdf)
self.closeBtn.clicked.connect(self.close)
self.closeBtn.clicked.connect(self.cbar.clear)
self.segmentationBtn.clicked.connect(self.onSegmentationBtn)
self.slider.newValue.connect(self.showObjects)
self.slider.valueChanged.connect(self.showImage)
self.slider.sliderReleased.connect(self.showObjects)
self.slider.sliderPressed.connect(self.cbar.clearContours)
self.contoursCb.stateChanged.connect(self.onContours)
self.showBBoxes.stateChanged.connect(self.onBBoxes)
self.showBBoxes.stateChanged.connect(self.showObjects)
self.segdlg.paramsChanged.connect(self.showObjects)
self.segdlg.refreshBtn.clicked.connect(self.showObjects)
self.segdlg.imageUpdate.connect(self.showImage)
self.segdlg.activateChannels.connect(self.cbar.activateChannels)
self.segdlg.changeColor.connect(self.cbar.setColor)
self.nextBtn.clicked.connect(self.onNextBtn)
self.prevBtn.clicked.connect(self.onPrevBtn)
def __init__(self, *args, **kw):
super(SegmentationDialog, self).__init__(*args, **kw)
loadUI(splitext(__file__)[0]+'.ui', self)
self.setWindowFlags(Qt.Tool)
# row count (rowCount from gridlayout is not reliable!)
self._rcount = 1
self.pchannel.currentIndexChanged[str].connect(self.onChannelChanged)
self.loadBtn.clicked.connect(self.onLoadBtn)
self.saveBtn.clicked.connect(self.onSaveBtn)
self.watershed.stateChanged.connect(self.emitParamsChanged)
self.zsliceMethod.addItems(ZProject.names())
self.zsliceMethod.currentIndexChanged.connect(
self.onZSliceMethodChanged)
self.zslice.valueChanged.connect(self.emitImageUpdate)
def __init__(self, *args, **kw):
super(AtSortWidget, self).__init__(*args, **kw)
uifile = join(dirname(__file__), self.__class__.__name__ + ".ui")
loadUI(uifile, self)
self.treeview.activated.connect(self.onActivated)
self.sortAlgorithm.addItems(Sorter.sorters())
self.model = AtSorterItemModel(self)
self.treeview.setModel(self.model)
self.setupToolBar()
self.startSorting.connect(
lambda: self.tileview.reorder(force_update=True))
self._channels = tuple()
def __init__(self, *args, **kw):
super(AtSortWidget, self).__init__(*args, **kw)
uifile = join(dirname(__file__), self.__class__.__name__ + ".ui")
loadUI(uifile, self)
self.treeview.activated.connect(self.onActivated)
self.sortAlgorithm.addItems(Sorter.sorters())
self.model = AtSorterItemModel(self)
self.treeview.setModel(self.model)
self.setupToolBar()
self.startSorting.connect(
lambda: self.tileview.reorder(force_update=True))
self._channels = tuple()
def __init__(self, *args, **kw):
super(AtFeatureSelectionDlg, self).__init__(*args, **kw)
uifile = splitext(__file__)[0] + ".ui"
loadUI(uifile, self)
self.setWindowFlags(Qt.Window)
self.regexLbl.setBuddy(self.regex)
self.regex.textChanged.connect(self.filterChanged)
self.proxyModel = AtSortFilterProxyModel()
self.proxyModel.setDynamicSortFilter(False)
self.view.setModel(self.proxyModel)
self.model = AtFeatureModel(self)
self.setSourceModel(self.model)
self.selectAll.stateChanged.connect(self.toggleAll)
self.selectedOnly.stateChanged.connect(self.view.model().setStateFilter)
self.selectionChanged.connect(self.setSelectionByName)
def __init__(self, items, classes, exclude_training_data=True, *args, **kw):
super(BarGraph, self).__init__(*args, **kw)
loadUI(splitext(__file__)[0]+'.ui', self)
self.setWindowTitle("Counts grouped by Treatment")
self._exclude_td = exclude_training_data
self._items = items
counter = lambda: defaultdict(lambda: 0)
treatments = defaultdict(counter)
class_counts = dict()
for item in self._items:
if self._exclude_td and item.isTrainingSample():
continue
treatments[item.treatment][item.class_.name] += 1
class_counts[item.class_.label] = item.class_.name
self._plot(class_counts, treatments, classes)
def __init__(self, *args, **kw):
super(AtAnnotationWidget, self).__init__(*args, **kw)
uifile = join(dirname(__file__), self.__class__.__name__ + ".ui")
loadUI(uifile, self)
self._classifier_is_valid = False
self._prediction_is_valid = False
self._modified = True
self.saveBtn.clicked.connect(self.onSave)
self.loadBtn.clicked.connect(self.onLoadAnnotations)
self._setupClassifiers()
self.classifiers.currentIndexChanged.connect(
self.classifierChanged)
self.tileview.emitSelectedItems.connect(
self.selectByHashes)
def __init__(self, files, *args, **kw):
super(ImageDims, self).__init__(*args, **kw)
loadUI(splitext(__file__)[0]+'.ui', self)
self.files = files
self.example.setText("Example: %s" %basename(files[0].file))
self.separator.returnPressed.connect(self.updateRegex)
self.coord1.returnPressed.connect(self.updateRegex)
self.coord2.returnPressed.connect(self.updateRegex)
self.regex.returnPressed.connect(self.updateTree)
self.coord1Cb.currentIndexChanged.connect(self.updateRegex)
self.coord2Cb.currentIndexChanged.connect(self.updateRegex)
self._restoreSettings()
self.updateRegex()
def __init__(self, items, indices, classes, title="", exclude_training_data=True, *args, **kw):
super(BoxPlot, self).__init__(*args, **kw)
loadUI(splitext(__file__)[0]+'.ui', self)
self.setWindowTitle(title)
self._exclude_td = exclude_training_data
self._tabs = dict()
self._items = items
values = lambda: defaultdict(list)
data = defaultdict(values)
for ch, idx in indices.iteritems():
for item in self._items:
if self._exclude_td and item.isTrainingSample():
continue
value = item.features[idx]
data[item.treatment][item.class_.name].append(value)
self._plot(cn.from_abreviation(ch), title, data, classes)
def __init__(self, *args, **kw):
super(AtAnnotationWidget, self).__init__(*args, **kw)
uifile = join(dirname(__file__), self.__class__.__name__ + ".ui")
loadUI(uifile, self)
self._classifier_is_valid = False
self.saveBtn.clicked.connect(self.onSave)
self.loadBtn.clicked.connect(self.onLoadAnnotations)
self._setupClassifiers()
self.classifiers.currentIndexChanged.connect(
self.classifierChanged)
self.removeBtn.clicked.connect(self.removeSelected)
self.removeAllBtn.clicked.connect(self.removeAll)
self.predictBtn.clicked.connect(self.onPredict)
self.predictBtn.setText('Predict')
self.tileview.emitSelectedItems.connect(
self.selectByHashes)
def __init__(self, *args, **kw):
super(AtPreferencesDialog, self).__init__(*args, **kw)
loadUI(splitext(__file__)[0]+'.ui', self)
self.setWindowTitle("Preferences")
self._compopts_old = dict()
for name, value in BatchSizes.iteritems():
self.batchsize.addItem(name, value)
self.loadSettings()
self.accepted.connect(self.saveSettings)
validator = QtGui.QRegExpValidator(QtCore.QRegExp("^\d+(,\d+)*$"))
self.haralickDist.setValidator(validator)
self.granulometrySizes.setValidator(validator)
self.hdf_compression.currentIndexChanged[str].connect(
self.updateCompressionOptions)
self.hdf_compopts.currentIndexChanged[str].connect(
self.compoptsUpdated)
def __init__(self, parent, classifier, *args, **kw):
super(CrossValidationDialog, self).__init__(parent=parent, *args, **kw)
loadUI(splitext(__file__)[0] + '.ui', self)
self.setWindowFlags(Qt.Window)
self.classifier = classifier
self._tabs = dict()
self.applyBtn.clicked.connect(self.onApplyBtn)
self.okBtn.clicked.connect(self.onOkBtn)
self.crossValBtn.clicked.connect(self.onCrossValiation)
self.gridSearchBtn.clicked.connect(self.onGridSearch)
self.gridSearchFinished.connect(self.crossValidation)
self.gridSearchFinished.connect(self.onApplyBtn)
self.gridSearchFinished.connect(parent.predictionInvalid)
self.requestDataUpdate.connect(self.updateData)
self.features = None
self.labels = None
self.confusion_matrix = None
self.onGridSearch()
def __init__(self, parent, classifier, *args, **kw):
super(CrossValidationDialog, self).__init__(parent=parent, *args, **kw)
loadUI(splitext(__file__)[0] + ".ui", self)
self.setWindowFlags(Qt.Window)
self.classifier = classifier
self._tabs = dict()
self.applyBtn.clicked.connect(self.onApplyBtn)
self.okBtn.clicked.connect(self.onOkBtn)
self.crossValBtn.clicked.connect(self.onCrossValiation)
self.gridSearchBtn.clicked.connect(self.onGridSearch)
self.gridSearchFinished.connect(self.crossValidation)
self.gridSearchFinished.connect(self.onApplyBtn)
self.gridSearchFinished.connect(parent.predictionInvalid)
self.requestDataUpdate.connect(self.updateData)
self.features = None
self.labels = None
self.confusion_matrix = None
self.onGridSearch()
def __init__(self, parent, range_=(0, 256)):
super(AtContrastSliderWidget, self).__init__(parent)
loadUI(splitext(__file__)[0]+'.ui', self)
self.settings = BaCCalculator(*range_)
self.minimum.setRange(*range_)
self.maximum.setRange(*range_)
self.brightness.setRange(*range_)
self.contrast.setRange(*range_)
self.settings.valuesUpdated.connect(self.updateSliders)
self.minMaxBtn.clicked.connect(self.settings.setImageToMinMax)
self.resetBtn.clicked.connect(self.settings.reset)
self.autoBtn.clicked.connect(self.settings.setAuto)
self.autoBtn.setToolTip("Cuts of 1% of the histogram")
self.minimum.valueChanged.connect(self.settings.setMinimum)
self.maximum.valueChanged.connect(self.settings.setMaximum)
self.contrast.valueChanged.connect(self.settings.setContrast)
self.brightness.valueChanged.connect(self.settings.setBrightness)
self.minimum.valueChanged.connect(self.valuesToolTip)
self.maximum.valueChanged.connect(self.valuesToolTip)
self.contrast.valueChanged.connect(self.valuesToolTip)
self.brightness.valueChanged.connect(self.valuesToolTip)
self.minimum.sliderReleased.connect(self.sliderReleased.emit)
self.maximum.sliderReleased.connect(self.sliderReleased.emit)
self.contrast.sliderReleased.connect(self.sliderReleased.emit)
self.brightness.sliderReleased.connect(self.sliderReleased.emit)
self.minMaxBtn.clicked.connect(self.buttonClicked.emit)
self.resetBtn.clicked.connect(self.buttonClicked.emit)
self.autoBtn.clicked.connect(self.buttonClicked.emit)
self.buttonClicked.connect(self.valuesToolTip)
self.updateSliders()
def __init__(self, *args, **kw):
super(ExpansionWidget, self).__init__(*args, **kw)
loadUI(join(dirname(__file__), "expansionregion.ui"), self)
def __init__(self, parent, *args, **kw):
super(HoneyCombWidget, self).__init__(parent, *args, **kw)
loadUI(splitext(__file__)[0]+'.ui', self)
def __init__(self, collections_file, *args, **kw):
if not isfile(collections_file):
collections_file = join("doc", basename(collections_file))
collections_file = create_temporary_copy(collections_file)
if not isfile(collections_file):
raise IOError("%s file not found" % (collections_file))
super(AtAssistant, self).__init__(*args, **kw)
loadUI(join(dirname(__file__), "assistant.ui"), self)
self.hengine = QtHelp.QHelpEngine(collections_file)
self.hengine.setupData()
self.hengine.registerDocumentation(
collections_file.replace('.qhc', '.qch'))
self.hengine.searchEngine().reindexDocumentation()
self.hbrowser = AtHelpBrowser()
self.hbrowser.setHelpEngine(self.hengine)
self.setCentralWidget(self.hbrowser)
self.hengine.contentWidget().linkActivated.connect(
self.hbrowser.setSource)
self._setupToolBar()
self.queries = self.hengine.searchEngine().queryWidget()
self.results = self.hengine.searchEngine().resultWidget()
self.index = self.hengine.indexWidget()
self.contents = self.hengine.contentWidget()
self.tabifyDockWidget(self.contentDock, self.indexDock)
self.tabifyDockWidget(self.contentDock, self.searchDock)
self.searchDock.hide()
# search dock (hidden)
search = QtWidgets.QFrame(self)
vbox = QtWidgets.QVBoxLayout(search)
vbox.setContentsMargins(3, 3, 3, 3)
vbox.addWidget(self.queries)
vbox.addWidget(self.results)
self.results.requestShowLink.connect(self.hbrowser.setSource)
self.index.linkActivated.connect(self.hbrowser.setSource)
self.queries.search.connect(self.search)
# index dock
index = QtWidgets.QFrame(self)
filterEdit = AtLineEdit(self)
vbox = QtWidgets.QVBoxLayout(index)
vbox.setContentsMargins(3, 3, 3, 3)
vbox.addWidget(QtWidgets.QLabel("Look for:"))
vbox.addWidget(filterEdit)
vbox.addWidget(self.index)
filterEdit.textChanged.connect(self.filter)
self.searchDock.setWidget(search)
self.contentDock.setWidget(self.contents)
self.indexDock.setWidget(index)
self._restoreSettings()
self.indexDock.show()
self.contentDock.show()
def __init__(self, *args, **kw):
super(SaveClassifierDialog, self).__init__(*args, **kw)
uifile = splitext(__file__)[0] + ".ui"
loadUI(uifile, self)
self.pathBtn.clicked.connect(self.onPathBtn)
def __init__(self, collections_file, *args, **kw):
if not isfile(collections_file):
collections_file = join("doc", basename(collections_file))
collections_file = create_temporary_copy(collections_file)
if not isfile(collections_file):
raise IOError("%s file not found" %(collections_file))
super(AtAssistant, self).__init__(*args, **kw)
loadUI(join(dirname(__file__), "assistant.ui"), self)
self.hengine = QtHelp.QHelpEngine(collections_file)
self.hengine.setupData()
self.hengine.registerDocumentation(
collections_file.replace('.qhc', '.qch'))
self.hengine.searchEngine().reindexDocumentation()
self.hbrowser = AtHelpBrowser()
self.hbrowser.setHelpEngine(self.hengine)
self.setCentralWidget(self.hbrowser)
self.hengine.contentWidget().linkActivated.connect(
self.hbrowser.setSource)
self._setupToolBar()
self.queries = self.hengine.searchEngine().queryWidget()
self.results = self.hengine.searchEngine().resultWidget()
self.index = self.hengine.indexWidget()
self.contents = self.hengine.contentWidget()
self.tabifyDockWidget(self.contentDock, self.indexDock)
self.tabifyDockWidget(self.contentDock, self.searchDock)
self.searchDock.hide()
# search dock (hidden)
search = QtWidgets.QFrame(self)
vbox = QtWidgets.QVBoxLayout(search)
vbox.setContentsMargins(3, 3, 3, 3)
vbox.addWidget(self.queries)
vbox.addWidget(self.results)
self.results.requestShowLink.connect(self.hbrowser.setSource)
self.index.linkActivated.connect(self.hbrowser.setSource)
self.queries.search.connect(self.search)
# index dock
index = QtWidgets.QFrame(self)
filterEdit = AtLineEdit(self)
vbox = QtWidgets.QVBoxLayout(index)
vbox.setContentsMargins(3, 3, 3, 3)
vbox.addWidget(QtWidgets.QLabel("Look for:"))
vbox.addWidget(filterEdit)
vbox.addWidget(self.index)
filterEdit.textChanged.connect(self.filter)
self.searchDock.setWidget(search)
self.contentDock.setWidget(self.contents)
self.indexDock.setWidget(index)
self._restoreSettings()
self.indexDock.show()
self.contentDock.show()
def __init__(self, parent, *args, **kw):
super(AdaptiveThresholdWidget, self).__init__(parent, *args, **kw)
loadUI(splitext(__file__)[0] + ".ui", self)
# controls that trigger interactive image update
self.watershed.stateChanged.connect(parent.emitParamsChanged)
def __init__(self, file_=None, *args, **kw):
super(AtMainWindow, self).__init__(*args, **kw)
loadUI(splitext(__file__)[0]+'.ui', self)
self.setWindowTitle(version.appstr)
self.setAcceptDrops(True)
self.featuredlg = AtFeatureSelectionDlg(self)
self.featuredlg.hide()
self.loaderThread = AtThread(self)
self.loader = AtLoader()
self._lastdir = expanduser("~")
try:
self.assistant = AtAssistant(MANUAL)
self.assistant.hide()
except IOError:
QMessageBox.information(self, "Information",
"Sorry help files are not installed")
self.setupToolbar()
self.tileview = AtGraphicsView(
parent=self,
gsize=self.navToolBar.galsize)
self.toolBar.valueChanged.connect(self.tileview.zoom)
self.toolBar.classification.stateChanged.connect(
self.tileview.toggleClassIndicators, Qt.QueuedConnection)
self.toolBar.masking.stateChanged.connect(
self.tileview.toggleMasks, Qt.QueuedConnection)
self.toolBar.outline.stateChanged.connect(
self.tileview.toggleOutlines, Qt.QueuedConnection)
self.toolBar.description.stateChanged.connect(
self.tileview.toggleDescription, Qt.QueuedConnection)
self.setCentralWidget(self.tileview)
self.setupDock()
self.setupProgressBar()
self.loader.fileOpened.connect(self.updateToolbars)
self.loader.progressUpdate.connect(self.updateProgressBar)
self.loader.itemLoaded.connect(self.tileview.addItem)
self.abort.connect(self.loader.abort)
self.actionNewFile.triggered.connect(self.newDataFile)
self.actionOpenHdf.triggered.connect(self.onFileOpen)
self.actionCloseHdf.triggered.connect(self.onFileClose)
self.actionPreferences.triggered.connect(self.onPreferences)
self.actionExportViewPanel.triggered.connect(self.saveImage)
self.actionSaveData2Csv.triggered.connect(self.saveData2Csv)
self.actionSaveCountingStats.triggered.connect(self.saveCountingStats)
self.actionAboutQt.triggered.connect(self.onAboutQt)
self.actionAboutAnnotationTool.triggered.connect(self.onAbout)
self.actionFeatureSelection.triggered.connect(
self.showFeatureDlg)
self.actionHelpManual.triggered.connect(self.onHelpManual)
self.actionShortcuts.triggered.connect(self.onHelpShortcuts)
self.actionRefresh.triggered.connect(self.refresh)
self.actionSelectAll.triggered.connect(
self.tileview.actionSelectAll.trigger)
self.actionInvertSelection.triggered.connect(
self.tileview.actionInvertSelection.trigger)
self.tileview.zoomChanged.connect(self.updateZoomFactor)
self.featuredlg.selectionChanged.connect(
self.annotation.predictionInvalid)
self.loader.started.connect(self.onLoadingStarted)
self.zoom = QtWidgets.QLabel('100%')
self.statusbar.insertPermanentWidget(0, self.zoom)
self.statusbar.insertPermanentWidget(1,
QtWidgets.QLabel('Number of items:'))
self.nitems = QtWidgets.QLabel('0')
self.statusbar.insertPermanentWidget(2, self.nitems)
self._restoreSettings()
self.navToolBar.hide()
self.show()
if file_ is not None:
self.loader.openFile(file_)
self.loadItems()
def __init__(self, *args, **kw):
super(ImportDialog, self).__init__(*args, **kw)
loadUI(splitext(__file__)[0] + ".ui", self)
self.zsliceMethod.addItems(ZProject.names())
self.zsliceMethod.currentIndexChanged.connect(self.onZSliceMethodChanged)
self.pool = None
self._pool_running = False
for name, scn in FileScanner.iterclasses():
self.structType.addItem(scn.icon(), name)
self.structType.setIconSize(QtCore.QSize(48, 24))
self._files = None
self._regex = None
self.progressBar.hide()
self.segdlg = SegmentationDialog(self)
self.segdlg.hide()
self.zslice.valueChanged.connect(self.segdlg.setZSlice)
self.segdlg.zslice.valueChanged.connect(self.zslice.setValue)
self.zsliceMethod.currentIndexChanged.connect(self.segdlg.zsliceMethod.setCurrentIndex)
self.segdlg.zsliceMethod.currentIndexChanged.connect(self.zsliceMethod.setCurrentIndex)
self.viewer.setSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.MinimumExpanding)
self.cbar = ChannelBar(self, self.viewer)
self.cbox.addWidget(self.cbar)
self.cbar.newPixmap.connect(self.viewer.showPixmap, Qt.DirectConnection)
self.cbar.newContourImage.connect(self.viewer.contourImage)
self.cbar.colorsChanged.connect(self.segdlg.updateRowColors)
self.dataFileBtn.clicked.connect(self.onOpenOutFile)
self.imageDirBtn.clicked.connect(self.onOpenImageDir)
self.startBtn.clicked.connect(self.raw2hdf)
self.closeBtn.clicked.connect(self.close)
self.closeBtn.clicked.connect(self.cbar.clear)
self.segmentationBtn.clicked.connect(self.onSegmentationBtn)
self.slider.newValue.connect(self.showObjects)
self.slider.valueChanged.connect(self.showImage)
self.slider.sliderReleased.connect(self.showObjects)
self.slider.sliderPressed.connect(self.cbar.clearContours)
self.contoursCb.stateChanged.connect(self.onContours)
self.showBBoxes.stateChanged.connect(self.onBBoxes)
self.showBBoxes.stateChanged.connect(self.showObjects)
self.segdlg.paramsChanged.connect(self.showObjects)
self.segdlg.refreshBtn.clicked.connect(self.showObjects)
self.segdlg.imageUpdate.connect(self.showImage)
self.segdlg.activateChannels.connect(self.cbar.activateChannels)
self.segdlg.changeColor.connect(self.cbar.setColor)
self.nextBtn.clicked.connect(self.onNextBtn)
self.prevBtn.clicked.connect(self.onPrevBtn)
self.reloadBtn.clicked.connect(self.onReloadBtn)
self.setProgressRange.connect(self.progressBar.setRange)
self.setProgress.connect(self.progressBar.setValue, Qt.DirectConnection)
def __init__(self, file_=None, *args, **kw):
super(AtMainWindow, self).__init__(*args, **kw)
loadUI(splitext(__file__)[0]+'.ui', self)
self.setWindowTitle(version.appstr)
self.setAcceptDrops(True)
self.featuredlg = AtFeatureSelectionDlg(self)
self.featuredlg.hide()
self.loaderThread = AtThread(self)
self.loader = AtLoader()
self._lastdir = expanduser("~")
try:
self.assistant = AtAssistant(MANUAL)
self.assistant.hide()
except IOError:
QMessageBox.information(self, "Information",
"Sorry help files are not installed")
self.setupToolbar()
self.tileview = AtGraphicsView(
parent=self,
gsize=self.navToolBar.galsize)
self.toolBar.valueChanged.connect(self.tileview.zoom)
self.toolBar.flagsChanged.connect(
self.tileview.setViewFlags, Qt.QueuedConnection)
self.setCentralWidget(self.tileview)
self.setupDock()
self.setupProgressBar()
self.loader.fileOpened.connect(self.updateToolbars)
self.loader.progressUpdate.connect(self.updateProgressBar)
self.loader.itemCountChanged.connect(self.batchToolBar.setItemCount)
self.loader.itemLoaded.connect(self.tileview.addItem)
self.abort.connect(self.loader.abort)
self.actionNewFile.triggered.connect(self.newDataFile)
self.actionOpenHdf.triggered.connect(self.onFileOpen)
self.actionCloseHdf.triggered.connect(self.onFileClose)
self.actionPreferences.triggered.connect(self.onPreferences)
# Data Export
self.actionExportViewPanel.triggered.connect(self.saveImage)
self.actionSaveData2Csv.triggered.connect(self.saveData2Csv)
self.actionSaveCountingStats.triggered.connect(self.saveCountingStats)
# Plots
self.actionGroupedByClass.triggered.connect(self.plotGroupedByClass)
self.actionGroupedByTreatment.triggered.connect(
self.plotGroupedByTreatment)
self.actionIntensity.triggered.connect(self.plotIntesity)
self.actionSize.triggered.connect(self.plotSize)
self.actionStdDev.triggered.connect(self.plotStdDev)
self.actionPlotAll.triggered.connect(self.plotAll)
self.actionAboutQt.triggered.connect(self.onAboutQt)
self.actionAboutAnnotationTool.triggered.connect(self.onAbout)
self.actionFeatureSelection.triggered.connect(
self.showFeatureDlg)
self.actionHelpManual.triggered.connect(self.onHelpManual)
self.actionShortcuts.triggered.connect(self.onHelpShortcuts)
self.actionGettingStarted.triggered.connect(self.onHelpGettingStarted)
self.actionRefresh.triggered.connect(self.refresh)
self.actionSelectAll.triggered.connect(
self.tileview.actionSelectAll.trigger)
self.actionInvertSelection.triggered.connect(
self.tileview.actionInvertSelection.trigger)
self.actionSelectByTreatment.triggered.connect(self.selectByTreatment)
self.tileview.zoomChanged.connect(self.updateZoomFactor)
self.tileview.quickSort.connect(self.sortToolBar.quickSortBtn.toggle)
self.tileview.quickSort.connect(self.onQuickSort)
self.featuredlg.selectionChanged.connect(
self.annotation.predictionInvalid)
self.loader.started.connect(self.onLoadingStarted)
self.zoom = QtWidgets.QLabel('100%')
self.statusbar.insertPermanentWidget(0, self.zoom)
self.statusbar.insertPermanentWidget(1,
QtWidgets.QLabel('Number of items:'))
self.nitems = QtWidgets.QLabel('0')
self.statusbar.insertPermanentWidget(2, self.nitems)
self._restoreSettings()
self.navToolBar.hide()
self.show()
if file_ is not None:
self.loader.openFile(file_)
self.loadItems()
